metadynamics combined with PCV

From: Anurag Sethi (anurag.sethi_at_gmail.com)
Date: Fri Jun 03 2011 - 12:14:18 CDT

Hi,

I am trying to run metadynamics with NAMD 2.8b1 to study conformational
changes associated with allostery in HIV envelope proteins. I would like to
use the approach suggested by the Parrinello group in which they combine
path-based methods with the approach of collective variables and apply
metadynamics to study coformational changes in small peptides (Branduardi,
et al., J. Chem. Phys., 126:054103 (2007)) and kinases (Berteotti, et al.,
J. Am. Chem. Soc., 131:244-150 (2009)). In this method, they identify a
putative path by generating a morphed path from the initial conformation (A)
to the final conformation (B). After this, they define two path collective
variables (PCVs). One of these PCVs (s in their notation) measures the
"progress" along the putative path while the other PCV (z in their notation)
measures the "distance" of the conformation from the putative path. Using
this method, they are able to find multiple pathways for conformational
changes using metadynamics (in combination with the nudged elastic band in
their case).

Both these PCVs use exponential functions of RMSD of the protein from
multiple conformations (defined by the putative path) of the protein. It is
equations 1 and 2 in the 2007 paper referenced above. I have read the
documentation for the colvars module in NAMD and see that RMSD is one of the
colvars defined in NAMD. However, I also see that polynomial functions of
these colvars can be used in NAMD directly. Is there any way for me to use
tcl along with NAMD to define these PCVs and run metadynamics on these PCVs?

Thanks for your help,
Anurag

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